From e62de94354b0e2c1239202b46a973b9be54ac628 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Fri, 20 Dec 2024 13:34:43 -0500 Subject: [PATCH 1/3] Bump version to 1.0.10, update poetry lock --- poetry.lock | 108 +++++++++++++++++++++++-------------------------- pyproject.toml | 2 +- 2 files changed, 51 insertions(+), 59 deletions(-) diff --git a/poetry.lock b/poetry.lock index 67a833677..4efdcbd59 100644 --- a/poetry.lock +++ b/poetry.lock @@ -499,17 +499,17 @@ files = [ [[package]] name = "boto3" -version = "1.35.84" +version = "1.35.85" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.35.84-py3-none-any.whl", hash = "sha256:c94fc8023caf952f8740a48fc400521bba167f883cfa547d985c05fda7223f7a"}, - {file = "boto3-1.35.84.tar.gz", hash = "sha256:9f9bf72d92f7fdd546b974ffa45fa6715b9af7f5c00463e9d0f6ef9c95efe0c2"}, + {file = "boto3-1.35.85-py3-none-any.whl", hash = "sha256:f22678bdbdc91ca6022a45696284d236e1fbafa84ca3a69d108d4a155cdd823e"}, + {file = "boto3-1.35.85.tar.gz", hash = "sha256:6257cad97d92c2b5597aec6e5484b9cfed8c0c785297942ed37cfaf2dd0ec23c"}, ] [package.dependencies] -botocore = ">=1.35.84,<1.36.0" +botocore = ">=1.35.85,<1.36.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -518,13 +518,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.35.84" +version = "1.35.85" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" files = [ - 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Harry Caufield "] license = "BSD-3" From 470ab466db1fba03fae8f2dcde9fba1295f98ee5 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Fri, 20 Dec 2024 13:37:22 -0500 Subject: [PATCH 2/3] Linting webapp --- src/ontogpt/webapp/html/form.html | 146 ++++++++++++++------------- src/ontogpt/webapp/html/results.html | 55 +++++----- 2 files changed, 105 insertions(+), 96 deletions(-) diff --git a/src/ontogpt/webapp/html/form.html b/src/ontogpt/webapp/html/form.html index ce447018a..d479da7fa 100644 --- a/src/ontogpt/webapp/html/form.html +++ b/src/ontogpt/webapp/html/form.html @@ -1,95 +1,105 @@ - - + + OntoGPT SPIRES: Enter text - - -
-
+ + +
+

Information Extraction with SPIRES

- Select Schema: - {% for key, value in datamodels.items() %} - + {% endfor %} - +
- Select LLM (non-GPT models will require ollama to be running): - + Select LLM (non-GPT models will require ollama to be running): +
- +
- +
- Loading... -
-
- GPT models use the OpenAI API and may incur costs. + Loading...
+
GPT models use the OpenAI API and may incur costs.
- Please be patient, can take up to 10s, or longer if ontology resources need to be retrieved and/or using large local models. + Please be patient, can take up to 10s, or longer if ontology + resources need to be retrieved and/or using large local models.
- -
-
-

Powered by OntoGPT

-
- + +
+
+

+ Powered by + OntoGPT +

+
+ diff --git a/src/ontogpt/webapp/html/results.html b/src/ontogpt/webapp/html/results.html index eff739eeb..91f5ce85a 100644 --- a/src/ontogpt/webapp/html/results.html +++ b/src/ontogpt/webapp/html/results.html @@ -1,33 +1,32 @@ - - - SPIRES: Results - - - -
- Try another! -
+ + + SPIRES: Results + + + +
+ Try another! +
+ + {{ inner_html|safe }} + From b4fd6a8c9b64ea92e92db6dd4f4f26be4ad14680 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Fri, 20 Dec 2024 13:39:02 -0500 Subject: [PATCH 3/3] Linting in utils --- src/ontogpt/utils/clinical_cases.py | 1 + src/ontogpt/utils/model_utils.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/src/ontogpt/utils/clinical_cases.py b/src/ontogpt/utils/clinical_cases.py index 0a7f334f0..8c2b84058 100644 --- a/src/ontogpt/utils/clinical_cases.py +++ b/src/ontogpt/utils/clinical_cases.py @@ -10,6 +10,7 @@ PMCID: PMC10273128 """ + def get_kanjee_prompt() -> str: """Prompt from Kanjee et al. 2023.""" prompt = ( diff --git a/src/ontogpt/utils/model_utils.py b/src/ontogpt/utils/model_utils.py index e0aabe726..0abd74971 100644 --- a/src/ontogpt/utils/model_utils.py +++ b/src/ontogpt/utils/model_utils.py @@ -1,4 +1,4 @@ -"""Utilities for retrieving and applying prebuild models.""" +"""Utilities for retrieving and applying prebuilt models.""" import logging from pathlib import PosixPath